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mibig-secmet / mibig-json

Repository to track changes in MIBiG curation data stored in JSON format
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Bad ranges in various metallophore BGCs #270

Open zreitz opened 1 year ago

zreitz commented 1 year ago

New cluster boundaries to match literature: BGC0002530: 9552..16349 BGC0002531: 1680959..1711406 BGC0002692: 1419402..1426027 BGC0001055: 16770..45600 BGC0002476: 609459..629713 BGC0002571: 2306144..2376631 BGC0002496: 3971313..3991082 BGC0002567: 44349..56279

These records have to be expanded by a few nucleotides to include a gene that got cut off (e.g., coordinates were <1..## and excluded). There’s probably more of these. BGC0002488: 1977282..1986533 BGC0002493: 2379864..2385957 BGC0002688: 6441896..6461884 BGC0002691: 197700..223090 BGC0002493: 2379864..2385957

Improvement: BGC0002687: Modify the record to use gene calling from the RefSeq record (NZ_CP012201.1) to fix pseudogenes

zreitz commented 1 year ago

BGC0002476: 609459.. 629713

BGC0000412: Replace partial cluster with complete one: AE004091.2[4721614..4746551] Ref for that: https://link.springer.com/article/10.1007/s10534-010-9399-9

mmzdouc commented 8 months ago

This issue is being addressed in the ongoing curation effort.